Mercurial > repos > refinery-platform > qualimap2_bamqc
changeset 0:a6d048668f7f draft
planemo upload for repository https://github.com/refinery-platform/qualimap2 commit 88b5467f336ac3b6b5d3a6e824273a183e5184b6
| author | refinery-platform |
|---|---|
| date | Mon, 30 Jul 2018 09:56:10 -0400 |
| parents | |
| children | f36ed3bfcfe6 |
| files | qualimap_bamqc.py qualimap_bamqc.xml test-data/test.bam tool_dependencies.xml |
| diffstat | 4 files changed, 107 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_bamqc.py Mon Jul 30 09:56:10 2018 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env python +from __future__ import print_function +import argparse +import os +from subprocess import check_call, CalledProcessError +import shutil +import sys + +QUALIMAP_OUPUT_DIR = "qualimap_results" + + +def qualimap_bamqc(bam_filename, jv_mem_size): + qualimap_command = [ + "qualimap", "bamqc", + "-bam " + bam_filename, + "-outdir " + QUALIMAP_OUPUT_DIR, + "--java-mem-size=" + jv_mem_size + ] + + try: + check_call(qualimap_command) + except CalledProcessError: + print("Error running the qualimap bamqc", file=sys.stderr) + + +def main(): + parser = argparse.ArgumentParser( + description="Generate Bam Quality Statistics" + ) + parser.add_argument('--input_file') + parser.add_argument('--out_dir') + parser.add_argument('--out_results') + parser.add_argument('--out_zip') + parser.add_argument('--java_mem_size') + + args = parser.parse_args() + + qualimap_bamqc(args.input_file, args.java_mem_size) + + shutil.make_archive( + 'raw_data_qualimapReport', + 'zip', + os.path.join(QUALIMAP_OUPUT_DIR, 'raw_data_qualimapReport') + ) + + shutil.move("raw_data_qualimapReport.zip", args.out_zip) + shutil.move( + os.path.join(QUALIMAP_OUPUT_DIR, "genome_results.txt"), + args.out_results + ) + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_bamqc.xml Mon Jul 30 09:56:10 2018 -0400 @@ -0,0 +1,48 @@ +<?xml version="1.0" encoding="utf-8" ?> +<tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2"> + <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description> + <requirements> + <requirement type="package" version="2.2">qualimap</requirement> + </requirements> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <command interpreter="python"> + qualimap_bamqc.py + --input_file $input_realigned_bam_file + --out_results $genome_results + --out_zip $raw_data_qualimapReport + --java_mem_size $mem_size + </command> + <inputs> + <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/> + <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/> + </inputs> + <outputs> + <data format="txt" name="genome_results" label="Qualimap BamQC Results for: ${input_realigned_bam_file}"></data> + <data format="zip" name="raw_data_qualimapReport" label="Qualimap Raw Data Results for: ${input_realigned_bam_file}"></data> + </outputs> + + <tests> + <test> + <param name="mem_size" value="2G"></param> + <param name="input_realigned_bam_file" value="test.bam"></param> + <output name="genome_results"> + <assert_contents> + <has_text text="BamQC report" /> + </assert_contents> + </output> + <output name="raw_data_qualimapReport" ftype="zip"> + <assert_contents> + <has_text text="" /> + </assert_contents> + </output> + </test> + </tests> + <help> + https://github.com/scottx611x/qualimap2 + </help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 30 09:56:10 2018 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="qualimap" version="2.2"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" changeset_revision="21698ad1bfb1" name="package_qualimap_2_2" owner="sanbi-uwc" /> + </package> +</tool_dependency> \ No newline at end of file